I don't know what you mean by multiple domain files. If you want www.yourdomain.com to go to one gallery and www.anotherdomain.com to go to another gallery at your Mac.com account, I don't believe you can do that at this time.

If you mean multiple photo galleries at www.yourdomain.com then yes, in the sense that they appear as different albums under your main gallery page.

Imagine I had three main web interests: music, work and sport and within each interest I had say five websites each

That means 15 websites in total

As I understand iWeb, I have to have all 15 websites running inside the same 'domain' file stored in library/application support/iweb. That seems a clunky, big file with all my eggs in one basket. Kinda like having all your documents in one big Word file

So I was wondering if I couldn't have three files/folders/whatever where I could store separately all the websites relating to my three areas of interest?

~/Library/Application Support/iWeb/Domain isn't a single file. It's a package containing a hierarchy or many folders and files. From the user's perspective the implementation should not be of too much interest as long as the functionality is what you want.

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